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test unicycler 0.4.8.0 #46

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jennaj opened this issue Jun 30, 2022 · 17 comments
Closed

test unicycler 0.4.8.0 #46

jennaj opened this issue Jun 30, 2022 · 17 comments

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@jennaj
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jennaj commented Jun 30, 2022

Reports of failures at the spades step in bugs

toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0
@jennaj
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jennaj commented Jun 30, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0

@mvdbeek
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mvdbeek commented Jun 30, 2022

Results (powered by Planemo)

Summary

State Count
Total 4
Passed 1
Error 1
Failure 2
Skipped 0
Errored s
Failed s
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)

    Problems:

    • Expecting value: line 1 column 1 (char 0)
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)

    Problems:

    • Expecting value: line 1 column 1 (char 0)
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Starting Unicycler (2022-06-30 17:37:53)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided only long reads, Unicycler will assemble the reads with miniasm and
then run repeated polishing rounds using Racon.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/unicycler -t 10 -o ./ --verbosity 3 --pilon_path /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_anchor_seg_len 10 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmers 21,23 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2

Unicycler version: v0.4.8
Using 10 threads

The output directory already exists and files may be reused or overwritten:
  /jetstream/scratch0/main/jobs/44272759/working

Dependencies:
  Program         Version   Status     Path                                                        
  spades.py                 not used                                                               
  racon           1.4.7     good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/racon                                              
  makeblastdb     2.9.0+    good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/makeblastdb                                        
  tblastn         2.9.0+    good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/tblastn                                            
  bowtie2-build             not used                                                               
  bowtie2                   not used                                                               
  samtools                  not used                                                               
  java                      not used                                                               
  pilon                     not used                                                               
  bcftools                  not used                                                               


Loading reads (2022-06-30 17:37:55)

0 / 40 (0.0%)
1 / 40 (2.5%) - 412 bp
2 / 40 (5.0%) - 4,847 bp
3 / 40 (7.5%) - 8,974 bp
4 / 40 (10.0%) - 13,249 bp
5 / 40 (12.5%) - 14,258 bp
6 / 40 (15.0%) - 14,806 bp
7 / 40 (17.5%) - 19,262 bp
8 / 40 (20.0%) - 19,737 bp
9 / 40 (22.5%) - 20,395 bp
10 / 40 (25.0%) - 32,024 bp
11 / 40 (27.5%) - 32,698 bp
12 / 40 (30.0%) - 34,509 bp
13 / 40 (32.5%) - 39,018 bp
14 / 40 (35.0%) - 43,351 bp
15 / 40 (37.5%) - 44,224 bp
16 / 40 (40.0%) - 45,978 bp
17 / 40 (42.5%) - 46,402 bp
18 / 40 (45.0%) - 61,596 bp
19 / 40 (47.5%) - 62,279 bp
20 / 40 (50.0%) - 63,700 bp
21 / 40 (52.5%) - 66,412 bp
22 / 40 (55.0%) - 66,845 bp
23 / 40 (57.5%) - 67,316 bp
24 / 40 (60.0%) - 69,428 bp
25 / 40 (62.5%) - 73,964 bp
26 / 40 (65.0%) - 75,608 bp
27 / 40 (67.5%) - 80,223 bp
28 / 40 (70.0%) - 84,810 bp
29 / 40 (72.5%) - 92,076 bp
30 / 40 (75.0%) - 92,832 bp
31 / 40 (77.5%) - 92,939 bp
32 / 40 (80.0%) - 93,532 bp
33 / 40 (82.5%) - 96,370 bp
34 / 40 (85.0%) - 100,656 bp
35 / 40 (87.5%) - 119,222 bp
36 / 40 (90.0%) - 123,827 bp
37 / 40 (92.5%) - 155,106 bp
38 / 40 (95.0%) - 156,254 bp
39 / 40 (97.5%) - 157,993 bp
40 / 40 (100.0%) - 162,406 bp
40 / 40 (100.0%) - 162,406 bp


Assembling contigs and long reads with miniasm (2022-06-30 17:37:55)
Saving to /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/01_assembly_reads.fastq:
  40 long reads

Finding overlaps with minimap... success
  120 overlaps

Assembling reads with miniasm... success
  7 segments, 6 links

    Unicycler removes any links from the string graph which create branches.
I.e. if any segment has two or more links connected to one end, those links are
removed. This will result in a graph with only simple linear paths that is
suitable for creating unambiguous bridges.

No links needed removal
Saving /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/11_branching_paths_removed.gfa
Merging segments into unitigs:

Linear unitig: 3708:125-4288- -> f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389-

  1 linear unitig
  total size = 5,836 bp
Saving /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/12_unitig_graph.gfa
Saving /jetstream/scratch0/main/jobs/44272759/working/002_unitig_graph.gfa


Polishing miniasm assembly with Racon (2022-06-30 17:38:22)
    Unicycler now uses Racon to polish the miniasm assembly. It does multiple
rounds of polishing to get the best consensus. Circular unitigs are rotated
between rounds such that all parts (including the ends) are polished well.

Saving to /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/racon_polish/polishing_reads.fastq:
  40 long reads

Polish       Assembly          Mapping
round            size          quality
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	210	4010	+	1	5836	1061	4603	1147	3800	255	cm:i:200
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	722	+	1	5836	5221	5833	179	612	255	cm:i:27
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	934	4391	-	1	5836	2376	5833	3457	3457	255	cm:i:1153
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	126	2525	-	1	5836	30	2314	787	2399	255	cm:i:144
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	280	4284	-	1	5836	4	3936	1481	4004	255	cm:i:246
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	2719	4286	-	1	5836	4215	5833	546	1618	255	cm:i:88
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	170	4027	+	1	5836	1680	5833	1032	4153	255	cm:i:174
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	2893	4082	+	1	5836	4	1602	220	1598	255	cm:i:30
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	1334	4566	-	1	5836	2699	5786	1281	3232	255	cm:i:243
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	98	2778	-	1	5836	50	2663	772	2680	255	cm:i:129
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	1225	4611	-	1	5836	2657	5833	1469	3386	255	cm:i:268
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	97	2786	-	1	5836	30	2636	905	2689	255	cm:i:157
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	143	4271	-	1	5836	338	4254	1834	4128	255	cm:i:470
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	3092	4330	-	1	5836	4503	5798	430	1295	255	cm:i:77
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	544	4408	-	1	5836	69	3927	1208	3864	255	cm:i:237
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	3008	4472	-	1	5836	4215	5748	351	1533	255	cm:i:53
a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template	433	106	396	+	1	5836	2909	3222	131	313	255	cm:i:22
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	335	4397	+	1	5836	1321	5257	1351	4062	255	cm:i:280
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	3437	4349	+	1	5836	23	961	238	938	255	cm:i:40
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	537	+	1	5836	5334	5798	154	464	255	cm:i:26
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	111	4359	-	1	5836	1673	5798	2062	4248	255	cm:i:487
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	109	1619	-	1	5836	30	1525	472	1510	255	cm:i:68
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	93	4048	+	1	5836	1733	5833	1303	4100	255	cm:i:230
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	2532	4244	+	1	5836	4	1690	311	1712	255	cm:i:43
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	289	4205	+	1	5836	23	3939	1039	3916	255	cm:i:166
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	296	1782	+	1	5836	4242	5798	367	1556	255	cm:i:63
begin           5,836             5.33
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	4010	+	1	6290	1009	5054	2431	4045	255	cm:i:529
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	722	+	1	6290	5670	6287	297	617	255	cm:i:63
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	3632	4010	+	1	6290	4	404	122	400	255	cm:i:19
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	934	4391	-	1	6290	2540	6287	2249	3747	255	cm:i:527
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	126	2508	-	1	6290	51	2474	1276	2423	255	cm:i:245
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	110	4284	-	1	6290	4	4316	2322	4312	255	cm:i:486
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	2719	4590	-	1	6290	4354	6287	943	1933	255	cm:i:194
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	116	4027	+	1	6290	1774	6287	2145	4513	255	cm:i:426
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	2893	4124	+	1	6290	4	1741	421	1737	255	cm:i:61
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	1345	4580	-	1	6290	2854	6226	2257	3372	255	cm:i:501
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	98	2778	-	1	6290	51	2831	1459	2780	255	cm:i:289
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	1225	4611	-	1	6290	2825	6287	2268	3462	255	cm:i:513
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	97	2745	-	1	6290	74	2805	1501	2731	255	cm:i:289
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	140	4284	-	1	6290	354	4699	2022	4345	255	cm:i:377
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	3069	4304	-	1	6290	4984	6271	614	1287	255	cm:i:117
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	138	4408	-	1	6290	72	4534	1921	4462	255	cm:i:337
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	3002	4533	-	1	6290	4597	6206	580	1609	255	cm:i:103
a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template	433	106	396	+	1	6290	3083	3386	169	303	255	cm:i:32
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	4397	+	1	6290	1126	5708	2368	4582	255	cm:i:487
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	3437	4392	+	1	6290	23	1039	362	1016	255	cm:i:59
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	539	+	1	6290	5785	6254	217	469	255	cm:i:45
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	4374	-	1	6290	1806	6258	2777	4452	255	cm:i:600
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	1578	-	1	6290	74	1603	761	1529	255	cm:i:150
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	122	795	+	1	6290	5209	5912	149	703	255	cm:i:24
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	149	847	+	1	6290	585	1307	155	722	255	cm:i:17
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	93	4048	+	1	6290	1886	6287	2070	4401	255	cm:i:456
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	2532	4244	+	1	6290	4	1838	656	1834	255	cm:i:109
c2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template	1148	97	391	+	1	6290	2060	2358	156	298	255	cm:i:35
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	289	4485	+	1	6290	23	4436	2106	4413	255	cm:i:421
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	111	1803	+	1	6290	4488	6273	744	1785	255	cm:i:131
1               6,290             7.82
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	4010	+	1	6242	1016	5009	2460	3993	255	cm:i:530
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	722	+	1	6242	5626	6239	283	613	255	cm:i:61
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	3632	4010	+	1	6242	4	408	117	404	255	cm:i:18
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	934	4391	-	1	6242	2535	6239	2234	3704	255	cm:i:514
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	126	2508	-	1	6242	51	2469	1387	2418	255	cm:i:271
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	110	4284	-	1	6242	4	4276	2380	4272	255	cm:i:494
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	2719	4590	-	1	6242	4314	6239	955	1925	255	cm:i:196
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	108	4027	+	1	6242	1759	6239	2194	4480	255	cm:i:440
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	2893	4124	+	1	6242	4	1735	450	1731	255	cm:i:67
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	1345	4580	-	1	6242	2848	6178	2284	3330	255	cm:i:509
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	98	2778	-	1	6242	51	2825	1504	2774	255	cm:i:295
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	1225	4611	-	1	6242	2819	6239	2235	3420	255	cm:i:510
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	109	2745	-	1	6242	74	2787	1517	2713	255	cm:i:304
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	140	4284	-	1	6242	358	4659	2051	4301	255	cm:i:391
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	3069	4304	-	1	6242	4939	6223	618	1284	255	cm:i:114
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	138	4408	-	1	6242	72	4493	1941	4421	255	cm:i:345
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	3002	4533	-	1	6242	4556	6158	579	1602	255	cm:i:105
a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template	433	106	396	+	1	6242	3077	3380	169	303	255	cm:i:32
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	4397	+	1	6242	1133	5664	2405	4531	255	cm:i:507
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	3437	4397	+	1	6242	23	1051	353	1028	255	cm:i:59
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	107	539	+	1	6242	5759	6206	204	447	255	cm:i:40
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	4374	-	1	6242	1799	6210	2749	4411	255	cm:i:591
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	1578	-	1	6242	74	1601	795	1527	255	cm:i:165
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	122	847	+	1	6242	5166	5916	224	750	255	cm:i:35
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	160	847	+	1	6242	602	1310	144	708	255	cm:i:16
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	124	4048	+	1	6242	1908	6239	2061	4331	255	cm:i:454
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	2532	4244	+	1	6242	4	1831	667	1827	255	cm:i:111
c2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template	1148	97	391	+	1	6242	2053	2352	157	299	255	cm:i:37
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	289	4485	+	1	6242	23	4395	2130	4372	255	cm:i:425
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	111	1803	+	1	6242	4447	6225	762	1778	255	cm:i:138
2               6,242             8.02
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	4010	+	1	6265	1028	5025	2436	3997	255	cm:i:527
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	722	+	1	6265	5642	6262	281	620	255	cm:i:59
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	3632	4010	+	1	6265	4	408	105	404	255	cm:i:17
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	934	4391	-	1	6265	2544	6262	2228	3718	255	cm:i:507
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	126	2508	-	1	6265	51	2478	1353	2427	255	cm:i:260
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	110	4284	-	1	6265	4	4293	2377	4289	255	cm:i:492
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	2719	4590	-	1	6265	4331	6262	967	1931	255	cm:i:194
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	108	4027	+	1	6265	1772	6262	2190	4490	255	cm:i:436
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	2893	4124	+	1	6265	4	1748	448	1744	255	cm:i:62
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	1345	4580	-	1	6265	2857	6201	2270	3344	255	cm:i:503
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	98	2778	-	1	6265	51	2834	1463	2783	255	cm:i:284
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	1225	4611	-	1	6265	2828	6262	2251	3434	255	cm:i:515
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	102	2745	-	1	6265	74	2804	1511	2730	255	cm:i:305
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	140	4284	-	1	6265	358	4676	2063	4318	255	cm:i:392
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	3069	4328	-	1	6265	4930	6246	623	1316	255	cm:i:113
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	138	4408	-	1	6265	72	4510	1987	4438	255	cm:i:350
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	3002	4533	-	1	6265	4573	6181	569	1608	255	cm:i:102
a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template	433	106	396	+	1	6265	3089	3392	169	303	255	cm:i:32
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	4397	+	1	6265	1145	5680	2423	4535	255	cm:i:509
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	3437	4397	+	1	6265	23	1063	337	1040	255	cm:i:56
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	107	539	+	1	6265	5779	6229	223	450	255	cm:i:45
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	4374	-	1	6265	1812	6233	2769	4421	255	cm:i:601
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	105	1578	-	1	6265	74	1615	764	1541	255	cm:i:156
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	122	847	+	1	6265	5182	5936	236	754	255	cm:i:36
bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template	1421	149	847	+	1	6265	589	1322	155	733	255	cm:i:17
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	124	4048	+	1	6265	1921	6262	2062	4341	255	cm:i:449
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	2532	4244	+	1	6265	4	1844	660	1840	255	cm:i:111
c2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template	1148	97	391	+	1	6265	2063	2361	157	298	255	cm:i:37
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	289	4485	+	1	6265	23	4412	2182	4389	255	cm:i:436
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	111	1803	+	1	6265	4464	6248	787	1784	255	cm:i:141
3               6,265             8.04

Best polish: /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/racon_polish/016_rotated.fasta
Saving /jetstream/scratch0/main/jobs/44272759/working/miniasm_assembly/13_racon_polished.gfa
Saving /jetstream/scratch0/main/jobs/44272759/working/003_racon_polished.gfa


Assembly complete (2022-06-30 17:39:05)
Saving /jetstream/scratch0/main/jobs/44272759/working/assembly.gfa


      

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    Job Parameters:
    

      

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Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "false"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

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  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
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Total
4




Passed
3




Error
1




Failure
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  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Command Line:
    

      

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    Exit Code:
    

      

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      0
      

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    Standard Output:
    

      

    • 

      Starting Unicycler (2022-09-15 20:11:02)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided only short reads, Unicycler will essentially function as a SPAdes-
optimiser. It will try many k-mer sizes, choose the best based on contig length
and graph connectivity, and scaffold the graph using SPAdes repeat resolution.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/unicycler -t 6 -o ./ --verbosity 3 --pilon_path /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2

Unicycler version: v0.4.8
Using 6 threads

The output directory already exists and files may be reused or overwritten:
  /corral4/main/jobs/045/766/45766283/working

Bridging mode: normal
  using default normal bridge quality cutoff: 10.00

Dependencies:
  Program         Version           Status     Path                                                        
  spades.py       3.13.1            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/spades.py                                          
  racon                             not used                                                               
  makeblastdb     2.9.0+            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/makeblastdb                                        
  tblastn         2.9.0+            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/tblastn                                            
  bowtie2-build   2.3.5             good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/bowtie2-build                                      
  bowtie2         2.3.5             good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/bowtie2                                            
  samtools        1.9               good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/samtools                                           
  java            11.0.1-internal   good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/java                                               
  pilon           1.23              good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/share/pilon-1.23-1/pilon-1.23.jar                      
  bcftools                          not used                                                               


Choosing k-mer range for assembly (2022-09-15 20:11:06)
    Unicycler chooses a k-mer range for SPAdes based on the length of the input
reads. It uses a wide range of many k-mer sizes to maximise the chance of
finding an ideal assembly.

SPAdes maximum k-mer: 127
Median read length: 251
K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127


SPAdes assemblies (2022-09-15 20:11:06)
    Unicycler now uses SPAdes to assemble the short reads. It scores the
assembly graph for each k-mer using the number of contigs (fewer is better) and
the number of dead ends (fewer is better). The score function is 1/(c*(d+2)),
where c is the contig count and d is the dead end count.

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/spades.py -o /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 6 --only-assembler -1 /corral4/main/jobs/045/766/45766283/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766283/working/fq2.fastq

System information:
  SPAdes version: 3.13.1
  Python version: 3.7.3
  OS: Linux-4.18.0-372.19.1.el8_6.x86_64-x86_64-with-centos-8.6-Green_Obsidian
Output dir: /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/corral4/main/jobs/045/766/45766283/working/fq1.fastq']
      right reads: ['/corral4/main/jobs/045/766/45766283/working/fq2.fastq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/tmp
  Threads: 6
  Memory limit (in Gb): 125
======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/spades.log
===== Assembling started.
== Running assembler: K27
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/K27/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 125 Gb
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/dataset.info) with K=27
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 6
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  52)   SPAdes started
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  59)   Starting from stage: construction
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  66)   Two-step RR enabled: 0
  0:00:00.006     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.042     4M / 4M    INFO    General                 (read_converter.hpp        :  77)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.042     4M / 4M    INFO    General                 (read_converter.hpp        :  78)   Converting paired reads
  0:00:00.269    84M / 88M   INFO    General                 (binary_converter.hpp      : 117)   7925 reads written
  0:00:00.272     4M / 88M   INFO    General                 (read_converter.hpp        :  87)   Converting single reads
  0:00:00.494   148M / 172M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:00.494     4M / 172M  INFO    General                 (read_converter.hpp        :  95)   Converting merged reads
  0:00:00.619   148M / 172M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:00.645     4M / 172M  INFO    General                 (construction.cpp          : 111)   Max read length 251
  0:00:00.645     4M / 172M  INFO    General                 (construction.cpp          : 117)   Average read length 250.525
  0:00:00.645     4M / 172M  INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.662     4M / 172M  INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 36 files using 6 threads. This might take a while.
  0:00:00.669     4M / 172M  INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 131072
  0:00:00.669     4M / 172M  INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 6.94423 Gb
  0:00:00.669     4M / 172M  INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 1864135
  0:00:01.117     3G / 3G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:01.120    24M / 3G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 31700 reads
  0:00:01.120    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:01.391    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 35249 kmers in total.
  0:00:01.392    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:01.534    24M / 3G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:01.540    24M / 3G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:01.540    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 96 files using 6 threads. This might take a while.
  0:00:01.550    24M / 3G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 131072
  0:00:01.550    24M / 3G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 6.94314 Gb
  0:00:01.550    24M / 3G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 699050
  0:00:02.254     4G / 4G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 35249 kmers
  0:00:02.254     4G / 4G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 35249 kmers.
  0:00:02.261    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:03.175    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 34510 kmers in total.
  0:00:03.175    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:03.394    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:03.423    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:03.512    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 24880 bytes occupied (5.7676 bits per kmer).
  0:00:03.512    24M / 4G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:03.522    24M / 4G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:03.523    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:03.523    24M / 4G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:03.523    24M / 4G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:03.555    24M / 4G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   7414 28-mers were removed by early tip clipper
  0:00:03.555    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:03.564    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:03.577    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 2055 sequences extracted
  0:00:03.586    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:03.601    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:03.603    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:03.603    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:03.603    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:03.684    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 19616 bytes occupied (4.45198 bits per kmer).
  0:00:03.685    24M / 4G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:03.833    24M / 4G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:03.835    24M / 4G    INFO    General                 (construction.cpp          : 464)   Processed 4110 edges
  0:00:03.909    24M / 4G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:03.909    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 7
  0:00:03.909    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 695
  0:00:03.909    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 695. Coverage mad: 91.9212
  0:00:03.909    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:04.027    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:04.320    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:05.091    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:05.968    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:07.474    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:07.474    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418
  0:00:07.476    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 1
  0:00:07.476    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 275
  0:00:07.476    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 275
  0:00:07.476    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 5132
  0:00:07.476    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 671.577
  0:00:07.476    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 275
  0:00:07.476    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:07.476    24M / 4G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simpli
..
p   : 116)   Using SMOOTHING distance estimator
  0:00:20.293    24M / 4G    INFO    General                 (distance_estimation.cpp   :  34)   Filtering info
  0:00:20.293    24M / 4G    INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; index size: 2
  0:00:20.293    24M / 4G    INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering
  0:00:20.293    24M / 4G    INFO    General                 (distance_estimation.cpp   : 182)   Clearing raw paired index
  0:00:20.293    24M / 4G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Repeat Resolving
  0:00:20.293    24M / 4G    INFO    General                 (repeat_resolving.cpp      :  69)   Using Path-Extend repeat resolving
  0:00:20.293    24M / 4G    INFO    General                 (launcher.cpp              : 481)   ExSPAnder repeat resolving tool started
  0:00:20.342    24M / 4G    INFO    General                 (launcher.cpp              : 392)   Creating main extenders, unique edge length = 2000
  0:00:20.343    24M / 4G    INFO    General                 (extenders_logic.cpp       : 278)   Estimated coverage of library #0 is 350.708
  0:00:20.343    24M / 4G    INFO    General                 (extenders_logic.cpp       : 278)   Estimated coverage of library #0 is 350.708
  0:00:20.343    24M / 4G    INFO    General                 (extenders_logic.cpp       : 475)   Using 1 paired-end library
  0:00:20.343    24M / 4G    INFO    General                 (extenders_logic.cpp       : 476)   Using 1 paired-end scaffolding library
  0:00:20.343    24M / 4G    INFO    General                 (extenders_logic.cpp       : 477)   Using 0 single read libraries
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 420)   Total number of extenders is 3
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:00:20.343    24M / 4G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:00:20.343    24M / 4G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 427)   Closing gaps in paths
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 455)   Gap closing completed
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 286)   Traversing tandem repeats
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 296)   Traversed 0 loops
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:00:20.343    24M / 4G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:00:20.343    24M / 4G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:00:20.343    24M / 4G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:00:20.343    24M / 4G    INFO    General                 (launcher.cpp              : 534)   ExSPAnder repeat resolving tool finished
  0:00:20.343    24M / 4G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:00:20.343    24M / 4G    INFO    General                 (contig_output_stage.cpp   :  45)   Writing GFA to /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly//K127/assembly_graph_with_scaffolds.gfa
  0:00:20.365    24M / 4G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly//K127/before_rr.fasta
  0:00:20.381    24M / 4G    INFO    General                 (contig_output_stage.cpp   :  56)   Outputting FastG graph to /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly//K127/assembly_graph.fastg
  0:00:20.388    24M / 4G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly//K127/final_contigs.paths
  0:00:20.391    24M / 4G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly//K127/scaffolds.paths
  0:00:20.396    24M / 4G    INFO    General                 (launch.hpp                : 151)   SPAdes finished
  0:00:20.400    24M / 4G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 0 minutes 20 seconds
===== Assembling finished. Used k-mer sizes: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127
 * Assembled contigs are in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/contigs.fasta
 * Assembled scaffolds are in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/scaffolds.paths
 * Assembly graph is in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/assembly_graph.fastg
 * Assembly graph in GFA format is in /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa
======= SPAdes pipeline finished.
SPAdes log can be found here: /corral4/main/jobs/045/766/45766283/working/spades_assembly/assembly/spades.log
Thank you for using SPAdes!

Insert size mean: 367.3 bp
Insert size stdev: 37.3 bp


Cleaning k127 graph
Repair multi way junctions  (2022-09-15 20:16:29)
Filter by read depth        (2022-09-15 20:16:29)
Filter homopolymer loops    (2022-09-15 20:16:29)
Merge all possible          (2022-09-15 20:16:29)
Normalise read depths       (2022-09-15 20:16:29)
Remove zero length segments (2022-09-15 20:16:29)
Sort link order             (2022-09-15 20:16:29)
Graph cleaning finished     (2022-09-15 20:16:29)
Saving /corral4/main/jobs/045/766/45766283/working/spades_assembly/k127_assembly_graph.gfa

Repair multi way junctions  (2022-09-15 20:16:29)
Filter by read depth        (2022-09-15 20:16:29)
Filter homopolymer loops    (2022-09-15 20:16:29)
Merge all possible          (2022-09-15 20:16:29)
Normalise read depths       (2022-09-15 20:16:29)
Remove zero length segments (2022-09-15 20:16:29)
Sort link order             (2022-09-15 20:16:29)
Graph cleaning finished     (2022-09-15 20:16:29)
Saving /corral4/main/jobs/045/766/45766283/working/spades_assembly/k127_assembly_graph.gfa


SPAdes assembly graph summary (2022-09-15 20:16:29)
K-mer   Contigs   Links   Total length   N50     Longest contig   Dead ends   Score   
   27                                                                                 
   47                                                                                 
   63                                                                                 
   77                                                                                 
   89                                                                                 
   99                                                                                 
  107                                                                                 
  115                                                                                 
  121                                                                                 
  127         1       1          5,513   5,513            5,513           0   5.00e-01 <-best

Read depth filter: removed 0 contigs totalling 0 bp
Deleting /corral4/main/jobs/045/766/45766283/working/spades_assembly/


Determining graph multiplicity (2022-09-15 20:16:29)
    Multiplicity is the number of times a sequence occurs in the underlying
sequence. Single-copy contigs (those with a multiplicity of one, occurring only
once in the underlying sequence) are particularly useful.
    Multiplicity determination begins by identifying contigs which are clearly
single-copy because they are of low depth and do not have more than one link
per side.

Median depth of 10 longest contigs: 1.00


Initial single copy segments:
    1

    Unicycler now uses a greedy algorithm to propagate multiplicity through the
graph. For example, if two single-copy contigs merge together, the resulting
contig will get a multiplicity of two. When no more propagation is possible,
additional single-copy contigs are added and the process is repeated. This
allows for multiplicity to be correctly assigned to the chromosome (at the
median depth) but also for plasmids (which may be higher or lower in depth).

          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        
       FINDING NEW SINGLE-COPY        
          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        
REMOVING PROPAGATION TOLERANCE        
          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        

Saving /corral4/main/jobs/045/766/45766283/working/001_best_spades_graph.gfa


Cleaning graph (2022-09-15 20:16:29)
    Unicycler now performs various cleaning procedures on the graph to remove
overlaps and simplify the graph structure. The end result is a graph ready for
bridging.

Grouping graph edges based on overlap removal

0 / 2 (0.0%)
1 / 2 (50.0%)
2 / 2 (100.0%)

Removing graph overlaps

             Bases     Bases
           trimmed   trimmed
 Segment      from      from
  number     start       end
       1        63        64
Graph overlaps removed

Saving /corral4/main/jobs/045/766/45766283/working/002_overlaps_removed.gfa

    Unicycler now selects a set of anchor contigs from the single-copy contigs.
These are the contigs which will be connected via bridges to form the final
assembly.


1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)

Anchor segments:
    1


Creating SPAdes contig bridges (2022-09-15 20:16:30)
    SPAdes uses paired-end information to perform repeat resolution (RR) and
produce contigs from the assembly graph. SPAdes saves the graph paths
corresponding to these contigs in the contigs.paths file. When one of these
paths contains two or more anchor contigs, Unicycler can create a bridge from
the path.

No SPAdes contig bridges


Creating loop unrolling bridges (2022-09-15 20:16:30)
    When a SPAdes contig path connects an anchor contig with the middle contig
of a simple loop, Unicycler concludes that the sequences are contiguous (i.e.
the loop is not a separate piece of DNA). It then uses the read depth of the
middle and repeat contigs to guess the number of times to traverse the loop and
makes a bridge.

No loop unrolling bridges made
none found


Applying bridges (2022-09-15 20:16:30)
    Unicycler now applies to the graph in decreasing order of quality. This
ensures that when multiple, contradictory bridges exist, the most supported
option is used.

Bridge type   Start -> end   Path   Quality   Result

Saving /corral4/main/jobs/045/766/45766283/working/003_bridges_applied.gfa


Cleaning up leftover segments (2022-09-15 20:16:30)
Segments eligible for deletion:


Bridged assembly graph (2022-09-15 20:16:30)
    The assembly is now mostly finished and no more structural changes will be
made. Ideally the assembly graph should now have one contig per replicon and no
erroneous contigs (i.e a complete assembly). If there are more contigs, then
the assembly is not complete.

Saving /corral4/main/jobs/045/766/45766283/working/004_final_clean.gfa

Component   Segments   Links   Length   N50     Longest segment   Status  
        1          1       1    5,386   5,386             5,386   complete


Polishing assembly with Pilon (2022-09-15 20:16:30)
    Unicycler now conducts multiple rounds of Pilon in an attempt to repair any
remaining small-scale errors with the assembly.

Aligning reads to find appropriate insert size range...
  bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta
  bowtie2 -1 /corral4/main/jobs/045/766/45766283/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766283/working/fq2.fastq -x 0_insert_size_check.fasta --fast --threads 6 -I 0 -X 5000 -S 0_alignments.sam
Insert size 1st percentile:  263
Insert size 99th percentile: 450

Pilon polish round 1
  bowtie2-build 1_polish_input.fasta 1_polish_input.fasta
  bowtie2 --local --very-sensitive-local --threads 6 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /corral4/main/jobs/045/766/45766283/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766283/working/fq2.fastq
  samtools sort -@ 6 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam
  samtools index 1_paired_alignments.bam
  java -jar /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /corral4/main/jobs/045/766/45766283/working/pilon_polish --fix bases --frags 1_paired_alignments.bam
No Pilon changes

Saving /corral4/main/jobs/045/766/45766283/working/005_polished.gfa


Rotating completed replicons (2022-09-15 20:16:38)
    Any completed circular contigs (i.e. single contigs which have one link
connecting end to start) can have their start position changed without altering
the sequence. For consistency, Unicycler now searches for a starting gene (dnaA
or repA) in each such contig, and if one is found, the contig is rotated to
start with that gene on the forward strand.

Segment 1:
  makeblastdb -dbtype nucl -in replicon.fasta
  tblastn -db replicon.fasta -query /cvmfs/main.galaxyproject.org/deps/_conda/pkgs/unicycler-0.4.8-py37h8b12597_0/lib/python3.7/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1

Segment   Length   Depth   Starting gene   Position   Strand   Identity   Coverage
      1    5,386   1.00x   none found                                             


Assembly complete (2022-09-15 20:16:55)
Saving /corral4/main/jobs/045/766/45766283/working/assembly.gfa
Saving /corral4/main/jobs/045/766/45766283/working/assembly.fasta


      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102781726, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102781729, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Starting Unicycler (2022-09-15 20:09:40)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided both short and long reads, Unicycler will perform a hybrid assembly.
It will first use SPAdes to make a short-read assembly graph, and then it will
use various methods to scaffold that graph with the long reads.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/unicycler -t 6 -o ./ --verbosity 3 --pilon_path /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar -1 fq1.fastq -2 fq2.fastq -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --no_correct --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2

Unicycler version: v0.4.8
Using 6 threads

The output directory already exists and files may be reused or overwritten:
  /corral4/main/jobs/045/766/45766282/working

Bridging mode: normal
  using default normal bridge quality cutoff: 10.00

Dependencies:
  Program         Version           Status     Path                                                        
  spades.py       3.13.1            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/spades.py                                          
  racon           1.4.7             good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/racon                                              
  makeblastdb     2.9.0+            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/makeblastdb                                        
  tblastn         2.9.0+            good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/tblastn                                            
  bowtie2-build   2.3.5             good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/bowtie2-build                                      
  bowtie2         2.3.5             good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/bowtie2                                            
  samtools        1.9               good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/samtools                                           
  java            11.0.1-internal   good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/bin/java                                               
  pilon           1.23              good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                               .4.8/share/pilon-1.23-1/pilon-1.23.jar                      
  bcftools                          not used                                                               


Choosing k-mer range for assembly (2022-09-15 20:09:42)
    Unicycler chooses a k-mer range for SPAdes based on the length of the input
reads. It uses a wide range of many k-mer sizes to maximise the chance of
finding an ideal assembly.

SPAdes maximum k-mer: 127
Median read length: 251
K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127


SPAdes assemblies (2022-09-15 20:09:43)
    Unicycler now uses SPAdes to assemble the short reads. It scores the
assembly graph for each k-mer using the number of contigs (fewer is better) and
the number of dead ends (fewer is better). The score function is 1/(c*(d+2)),
where c is the contig count and d is the dead end count.

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/spades.py -o /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly -k 27,47,63,77,89,99,107,115,121,127 --threads 6 --only-assembler -1 /corral4/main/jobs/045/766/45766282/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766282/working/fq2.fastq

System information:
  SPAdes version: 3.13.1
  Python version: 3.7.3
  OS: Linux-3.10.0-1160.11.1.el7.x86_64-x86_64-with-centos-7.9.2009-Core
Output dir: /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/corral4/main/jobs/045/766/45766282/working/fq1.fastq']
      right reads: ['/corral4/main/jobs/045/766/45766282/working/fq2.fastq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [27, 47, 63, 77, 89, 99, 107, 115, 121, 127]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/tmp
  Threads: 6
  Memory limit (in Gb): 125
======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/spades.log
===== Assembling started.
== Running assembler: K27
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/K27/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 125 Gb
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/dataset.info) with K=27
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 6
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  52)   SPAdes started
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  59)   Starting from stage: construction
  0:00:00.000     4M / 4M    INFO    General                 (launch.hpp                :  66)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.034     4M / 4M    INFO    General                 (read_converter.hpp        :  77)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.034     4M / 4M    INFO    General                 (read_converter.hpp        :  78)   Converting paired reads
  0:00:00.348    84M / 88M   INFO    General                 (binary_converter.hpp      : 117)   7925 reads written
  0:00:00.357     4M / 88M   INFO    General                 (read_converter.hpp        :  87)   Converting single reads
  0:00:00.582   148M / 172M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:00.592     4M / 172M  INFO    General                 (read_converter.hpp        :  95)   Converting merged reads
  0:00:00.809   148M / 172M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:01.195     4M / 172M  INFO    General                 (construction.cpp          : 111)   Max read length 251
  0:00:01.195     4M / 172M  INFO    General                 (construction.cpp          : 117)   Average read length 250.525
  0:00:01.195     4M / 172M  INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:01.229     4M / 172M  INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 36 files using 6 threads. This might take a while.
  0:00:01.250     4M / 172M  INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 131072
  0:00:01.250     4M / 172M  INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 6.94423 Gb
  0:00:01.250     4M / 172M  INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 1864135
  0:00:02.704     3G / 3G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:02.709    24M / 3G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 31700 reads
  0:00:02.709    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:03.983    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 35249 kmers in total.
  0:00:03.983    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:04.554    24M / 3G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:04.571    24M / 3G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:04.571    24M / 3G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 96 files using 6 threads. This might take a while.
  0:00:04.585    24M / 3G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 131072
  0:00:04.585    24M / 3G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 6.94314 Gb
  0:00:04.585    24M / 3G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 699050
  0:00:07.728     4G / 4G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 35249 kmers
  0:00:07.729     4G / 4G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 35249 kmers.
  0:00:07.733    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:09.926    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 34510 kmers in total.
  0:00:09.927    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:11.109    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:11.167    24M / 4G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:11.459    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 24880 bytes occupied (5.7676 bits per kmer).
  0:00:11.459    24M / 4G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:11.473    24M / 4G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:11.479    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:11.479    24M / 4G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:11.479    24M / 4G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:11.528    24M / 4G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   7414 28-mers were removed by early tip clipper
  0:00:11.528    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:11.556    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:11.565    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 2055 sequences extracted
  0:00:11.573    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:11.629    24M / 4G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:11.652    24M / 4G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:11.655    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:11.655    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:11.687    24M / 4G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 19616 bytes occupied (4.45198 bits per kmer).
  0:00:11.687    24M / 4G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:11.987    24M / 4G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:11.998    24M / 4G    INFO    General                 (construction.cpp          : 464)   Processed 4110 edges
  0:00:12.021    24M / 4G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:12.021    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 7
  0:00:12.021    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 695
  0:00:12.021    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 695. Coverage mad: 91.9212
  0:00:12.021    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:12.118    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:12.365    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:13.006    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:13.872    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:15.387    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:15.387    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418
  0:00:15.389    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 1
  0:00:15.389    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 275
  0:00:15.389    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 275
  0:00:15.389    24M / 4G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 5132
  0:00:15.389    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 671.577
  0:00:15.389    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 275
  0:00:15.389    24M / 4G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:15.389   
..
  INFO    General                 (launch.hpp                : 151)   SPAdes finished
  0:00:14.408    24M / 4G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 0 minutes 14 seconds
===== Assembling finished. Used k-mer sizes: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127
 * Assembled contigs are in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/contigs.fasta
 * Assembled scaffolds are in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/scaffolds.paths
 * Assembly graph is in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/assembly_graph.fastg
 * Assembly graph in GFA format is in /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/assembly_graph_with_scaffolds.gfa
======= SPAdes pipeline finished.
SPAdes log can be found here: /corral4/main/jobs/045/766/45766282/working/spades_assembly/assembly/spades.log
Thank you for using SPAdes!

Insert size mean: 367.3 bp
Insert size stdev: 37.3 bp


Cleaning k127 graph
Repair multi way junctions  (2022-09-15 20:16:40)
Filter by read depth        (2022-09-15 20:16:40)
Filter homopolymer loops    (2022-09-15 20:16:40)
Merge all possible          (2022-09-15 20:16:40)
Normalise read depths       (2022-09-15 20:16:40)
Remove zero length segments (2022-09-15 20:16:40)
Sort link order             (2022-09-15 20:16:40)
Graph cleaning finished     (2022-09-15 20:16:40)
Saving /corral4/main/jobs/045/766/45766282/working/spades_assembly/k127_assembly_graph.gfa

Repair multi way junctions  (2022-09-15 20:16:40)
Filter by read depth        (2022-09-15 20:16:40)
Filter homopolymer loops    (2022-09-15 20:16:40)
Merge all possible          (2022-09-15 20:16:40)
Normalise read depths       (2022-09-15 20:16:40)
Remove zero length segments (2022-09-15 20:16:40)
Sort link order             (2022-09-15 20:16:40)
Graph cleaning finished     (2022-09-15 20:16:40)
Saving /corral4/main/jobs/045/766/45766282/working/spades_assembly/k127_assembly_graph.gfa


SPAdes assembly graph summary (2022-09-15 20:16:40)
K-mer   Contigs   Links   Total length   N50     Longest contig   Dead ends   Score   
   27                                                                                 
   47                                                                                 
   63                                                                                 
   77                                                                                 
   89                                                                                 
   99                                                                                 
  107                                                                                 
  115                                                                                 
  121                                                                                 
  127         1       1          5,513   5,513            5,513           0   5.00e-01 <-best

Read depth filter: removed 0 contigs totalling 0 bp
Deleting /corral4/main/jobs/045/766/45766282/working/spades_assembly/


Determining graph multiplicity (2022-09-15 20:16:41)
    Multiplicity is the number of times a sequence occurs in the underlying
sequence. Single-copy contigs (those with a multiplicity of one, occurring only
once in the underlying sequence) are particularly useful.
    Multiplicity determination begins by identifying contigs which are clearly
single-copy because they are of low depth and do not have more than one link
per side.

Median depth of 10 longest contigs: 1.00


Initial single copy segments:
    1

    Unicycler now uses a greedy algorithm to propagate multiplicity through the
graph. For example, if two single-copy contigs merge together, the resulting
contig will get a multiplicity of two. When no more propagation is possible,
additional single-copy contigs are added and the process is repeated. This
allows for multiplicity to be correctly assigned to the chromosome (at the
median depth) but also for plasmids (which may be higher or lower in depth).

          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        
       FINDING NEW SINGLE-COPY        
          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        
REMOVING PROPAGATION TOLERANCE        
          MERGING MULTIPLICITY        
        SPLITTING MULTIPLICITY        

Saving /corral4/main/jobs/045/766/45766282/working/001_best_spades_graph.gfa


Cleaning graph (2022-09-15 20:16:41)
    Unicycler now performs various cleaning procedures on the graph to remove
overlaps and simplify the graph structure. The end result is a graph ready for
bridging.

Grouping graph edges based on overlap removal

0 / 2 (0.0%)
1 / 2 (50.0%)
2 / 2 (100.0%)

Removing graph overlaps

             Bases     Bases
           trimmed   trimmed
 Segment      from      from
  number     start       end
       1        63        64
Graph overlaps removed

Saving /corral4/main/jobs/045/766/45766282/working/002_overlaps_removed.gfa

    Unicycler now selects a set of anchor contigs from the single-copy contigs.
These are the contigs which will be connected via bridges to form the final
assembly.


1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp)

Anchor segments:
    1


Creating SPAdes contig bridges (2022-09-15 20:16:41)
    SPAdes uses paired-end information to perform repeat resolution (RR) and
produce contigs from the assembly graph. SPAdes saves the graph paths
corresponding to these contigs in the contigs.paths file. When one of these
paths contains two or more anchor contigs, Unicycler can create a bridge from
the path.

No SPAdes contig bridges


Creating loop unrolling bridges (2022-09-15 20:16:41)
    When a SPAdes contig path connects an anchor contig with the middle contig
of a simple loop, Unicycler concludes that the sequences are contiguous (i.e.
the loop is not a separate piece of DNA). It then uses the read depth of the
middle and repeat contigs to guess the number of times to traverse the loop and
makes a bridge.

No loop unrolling bridges made
none found


Loading reads (2022-09-15 20:16:41)

0 / 1 (0.0%)
1 / 1 (100.0%) - 5,386 bp
1 / 1 (100.0%) - 5,386 bp


Assembling contigs and long reads with miniasm (2022-09-15 20:16:41)
    Unicycler uses miniasm to construct a string graph assembly using both the
short read contigs and the long reads. It will then use the resulting string
graph to produce bridges between contigs. This method requires decent coverage
of long reads and therefore may not be fruitful if long reads are sparse.
However, it does not rely on the short read assembly graph having good
connectivity and is able to bridge an assembly graph even when it contains many
dead ends.
    Unicycler uses two types of "reads" as assembly input: anchor contigs from
the short-read assembly and actual long reads which overlap two or more of
these contigs. It then assembles them with miniasm.

Aligning long reads to graph using minimap
Saving /corral4/main/jobs/045/766/45766282/working/miniasm_assembly/all_segments.fasta
1	5386	3	5081	-	1	5386	4	5082	5078	5078	255	cm:i:1134
1	5386	5090	5383	-	1	5386	5088	5381	293	293	255	cm:i:63
Number of minimap alignments: 1

Saving to /corral4/main/jobs/045/766/45766282/working/miniasm_assembly/01_assembly_reads.fastq:
  0 short-read contigs
  1 long reads

Finding overlaps with minimap... failed
Assembling reads with miniasm... empty result


Creating simple long read bridges (2022-09-15 20:16:41)
    Unicycler uses long read alignments (from minimap) to resolve simple repeat
structures in the graph. This takes care of some "low-hanging fruit" of the
graph simplification.

Aligning long reads to graph using minimap
Saving /corral4/main/jobs/045/766/45766282/working/simple_bridging/all_segments.fasta
1	5386	3	5081	-	1	5386	4	5082	5078	5078	255	cm:i:1134
1	5386	5090	5383	-	1	5386	5088	5381	293	293	255	cm:i:63
Number of minimap alignments: 1

    Two-way junctions are defined as cases where two graph contigs (A and B)
join together (C) and then split apart again (D and E). This usually represents
a simple 2-copy repeat, and there are two possible options for its resolution:
(A->C->D and B->C->E) or (A->C->E and B->C->D). Each read which spans such a
junction gets to "vote" for option 1, option 2 or neither. Unicycler creates a
bridge at each junction for the most voted for option.

No suitable two-way junctions present

    Simple loops are parts of the graph where two contigs (A and B) are
connected via a repeat (C) which loops back to itself (via D). It is possible
to traverse the loop zero times (A->C->B), one time (A->C->D->C->B), two times
(A->C->D->C->D->C->B), etc. Long reads which span the loop inform which is the
correct number of times through. In this step, such reads are found and each is
aligned against alternative loop counts. A reads casts its "vote" for the loop
count it agrees best with, and Unicycler creates a bridge using the most voted
for count.

No suitable simple loops present


Determining low score threshold (2022-09-15 20:16:41)
    Before conducting semi-global alignment of the long reads to the assembly
graph, Unicycler must determine a minimum alignment score threshold such that
nonsense alignments are excluded. To choose a threshold automatically, it
examines alignments between random sequences and selects a score a few standard
deviations above the mean.

Automatically choosing a threshold using random alignment scores.

Random alignment mean score: 61.66
         standard deviation:  1.31
        Low score threshold: 61.66 + (7 x 1.31) = 70.86


Aligning reads with minimap (2022-09-15 20:16:41)
1	5386	5	5077	-	1	5386	8	5080	5072	5072	255	cm:i:945
1	5386	5093	5384	-	1	5386	5087	5378	291	291	255	cm:i:52

Done! 1 out of 1 reads aligned


Aligning reads (2022-09-15 20:16:41)
1/1: 1 (5386 bp)
minimap alignments:
    5,5077,-,1,8,5080
    5093,5384,-,1,5087,5378
Reference ranges:
    1-: 0 - 5386
Range: 1: 0 - 5386
    common 10-mers: 5464
    line 1: 5076 points, score=5074.000394 (good)
    line 2: 292 points, score=290.006826 (good)
All Seqan alignments (time to align = 0.086 s):
  Ref name  Ref start  Ref end  Read start  Read end  Strand  Raw score  Scaled score  Identity
         1          0     5085           0      5085       -      15255        100.00   100.00%
         1       5085     5386        5085      5386       -        903        100.00   100.00%
Final alignments:
  Ref name  Ref start  Ref end  Read start  Read end  Strand  Raw score  Scaled score  Identity
         1          0     5085           0      5085       -      15255        100.00   100.00%
         1       5085     5386        5085      5386       -        903        100.00   100.00%


Read alignment summary (2022-09-15 20:16:42)
Total read count:            1
Fully aligned reads:         1
Partially aligned reads:     0
Unaligned reads:             0
Total bases aligned:     5,386 bp
Mean alignment identity:   100.0%

Deleting /corral4/main/jobs/045/766/45766282/working/read_alignment/

Setting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00


Building long read bridges (2022-09-15 20:16:42)
    Unicycler uses the long read alignments to produce bridges between anchor
segments. These bridges can be formed using as few as one long read, giving
Unicycler the ability to bridge the graph even when long-read depth is low.

Median depth of 10 longest contigs: 1.00

                          Consensus  Consensus  Target                 Search    Path                                             Best path  Best path  Best path     Best path           
     Start -> end  Reads  len (bp)   time (s)   len (bp)  Search type  time (s)  count  Best path                                 len (bp)   raw score  scaled score  length disc  Quality


Applying bridges (2022-09-15 20:16:42)
    Unicycler now applies to the graph in decreasing order of quality. This
ensures that when multiple, contradictory bridges exist, the most supported
option is used.

Bridge type   Start -> end   Path   Quality   Result

Saving /corral4/main/jobs/045/766/45766282/working/003_bridges_applied.gfa


Cleaning up leftover segments (2022-09-15 20:16:42)
Segments eligible for deletion:


Bridged assembly graph (2022-09-15 20:16:42)
    The assembly is now mostly finished and no more structural changes will be
made. Ideally the assembly graph should now have one contig per replicon and no
erroneous contigs (i.e a complete assembly). If there are more contigs, then
the assembly is not complete.

Saving /corral4/main/jobs/045/766/45766282/working/004_final_clean.gfa

Component   Segments   Links   Length   N50     Longest segment   Status  
        1          1       1    5,386   5,386             5,386   complete


Polishing assembly with Pilon (2022-09-15 20:16:42)
    Unicycler now conducts multiple rounds of Pilon in an attempt to repair any
remaining small-scale errors with the assembly.

Aligning reads to find appropriate insert size range...
  bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta
  bowtie2 -1 /corral4/main/jobs/045/766/45766282/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766282/working/fq2.fastq -x 0_insert_size_check.fasta --fast --threads 6 -I 0 -X 5000 -S 0_alignments.sam
Insert size 1st percentile:  263
Insert size 99th percentile: 450

Pilon polish round 1
  bowtie2-build 1_polish_input.fasta 1_polish_input.fasta
  bowtie2 --local --very-sensitive-local --threads 6 -I 263 -X 450 -x 1_polish_input.fasta -S 1_paired_alignments.sam -1 /corral4/main/jobs/045/766/45766282/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766282/working/fq2.fastq
  samtools sort -@ 6 -o 1_paired_alignments.bam -O bam -T temp 1_paired_alignments.sam
  samtools index 1_paired_alignments.bam
  java -jar /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar --genome 1_polish_input.fasta --changes --output 1_pilon --outdir /corral4/main/jobs/045/766/45766282/working/pilon_polish --fix bases --frags 1_paired_alignments.bam
No Pilon changes

Pilon polish round 2
  bowtie2-build 2_polish_input.fasta 2_polish_input.fasta
  bowtie2 --local --very-sensitive-local --threads 6 -I 263 -X 450 -x 2_polish_input.fasta -S 2_paired_alignments.sam -1 /corral4/main/jobs/045/766/45766282/working/fq1.fastq -2 /corral4/main/jobs/045/766/45766282/working/fq2.fastq
  samtools sort -@ 6 -o 2_paired_alignments.bam -O bam -T temp 2_paired_alignments.sam
  samtools index 2_paired_alignments.bam
  java -jar /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar --genome 2_polish_input.fasta --changes --output 2_pilon --outdir /corral4/main/jobs/045/766/45766282/working/pilon_polish --fix all --frags 2_paired_alignments.bam
No Pilon changes

Saving /corral4/main/jobs/045/766/45766282/working/005_polished.gfa


Rotating completed replicons (2022-09-15 20:17:07)
    Any completed circular contigs (i.e. single contigs which have one link
connecting end to start) can have their start position changed without altering
the sequence. For consistency, Unicycler now searches for a starting gene (dnaA
or repA) in each such contig, and if one is found, the contig is rotated to
start with that gene on the forward strand.

Segment 1:
  makeblastdb -dbtype nucl -in replicon.fasta
  tblastn -db replicon.fasta -query /cvmfs/main.galaxyproject.org/deps/_conda/pkgs/unicycler-0.4.8-py37h8b12597_0/lib/python3.7/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1

Segment   Length   Depth   Starting gene   Position   Strand   Identity   Coverage
      1    5,386   1.00x   none found                                             


Assembly complete (2022-09-15 20:17:25)
Saving /corral4/main/jobs/045/766/45766282/working/assembly.gfa
Saving /corral4/main/jobs/045/766/45766282/working/assembly.fasta


      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102781726, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102781729, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Starting Unicycler (2022-09-15 20:09:18)
    Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you
provided only long reads, Unicycler will assemble the reads with miniasm and
then run repeated polishing rounds using Racon.
    For more information, please see https://github.com/rrwick/Unicycler

Command: /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/bin/unicycler -t 6 -o ./ --verbosity 3 --pilon_path /cvmfs/main.galaxyproject.org/deps/_conda/envs/[email protected]/share/pilon-1.23-1/pilon-1.23.jar -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_anchor_seg_len 10 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmers 21,23 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_polish_size 1000 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2

Unicycler version: v0.4.8
Using 6 threads

The output directory already exists and files may be reused or overwritten:
  /corral4/main/jobs/045/766/45766274/working

Dependencies:
  Program         Version   Status     Path                                                        
  spades.py                 not used                                                               
  racon           1.4.7     good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/racon                                              
  makeblastdb     2.9.0+    good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/makeblastdb                                        
  tblastn         2.9.0+    good       /cvmfs/main.galaxyproject.org/deps/_conda/envs/__unicycler@0
                                       .4.8/bin/tblastn                                            
  bowtie2-build             not used                                                               
  bowtie2                   not used                                                               
  samtools                  not used                                                               
  java                      not used                                                               
  pilon                     not used                                                               
  bcftools                  not used                                                               


Loading reads (2022-09-15 20:09:18)

0 / 40 (0.0%)
1 / 40 (2.5%) - 412 bp
2 / 40 (5.0%) - 4,847 bp
3 / 40 (7.5%) - 8,974 bp
4 / 40 (10.0%) - 13,249 bp
5 / 40 (12.5%) - 14,258 bp
6 / 40 (15.0%) - 14,806 bp
7 / 40 (17.5%) - 19,262 bp
8 / 40 (20.0%) - 19,737 bp
9 / 40 (22.5%) - 20,395 bp
10 / 40 (25.0%) - 32,024 bp
11 / 40 (27.5%) - 32,698 bp
12 / 40 (30.0%) - 34,509 bp
13 / 40 (32.5%) - 39,018 bp
14 / 40 (35.0%) - 43,351 bp
15 / 40 (37.5%) - 44,224 bp
16 / 40 (40.0%) - 45,978 bp
17 / 40 (42.5%) - 46,402 bp
18 / 40 (45.0%) - 61,596 bp
19 / 40 (47.5%) - 62,279 bp
20 / 40 (50.0%) - 63,700 bp
21 / 40 (52.5%) - 66,412 bp
22 / 40 (55.0%) - 66,845 bp
23 / 40 (57.5%) - 67,316 bp
24 / 40 (60.0%) - 69,428 bp
25 / 40 (62.5%) - 73,964 bp
26 / 40 (65.0%) - 75,608 bp
27 / 40 (67.5%) - 80,223 bp
28 / 40 (70.0%) - 84,810 bp
29 / 40 (72.5%) - 92,076 bp
30 / 40 (75.0%) - 92,832 bp
31 / 40 (77.5%) - 92,939 bp
32 / 40 (80.0%) - 93,532 bp
33 / 40 (82.5%) - 96,370 bp
34 / 40 (85.0%) - 100,656 bp
35 / 40 (87.5%) - 119,222 bp
36 / 40 (90.0%) - 123,827 bp
37 / 40 (92.5%) - 155,106 bp
38 / 40 (95.0%) - 156,254 bp
39 / 40 (97.5%) - 157,993 bp
40 / 40 (100.0%) - 162,406 bp
40 / 40 (100.0%) - 162,406 bp


Assembling contigs and long reads with miniasm (2022-09-15 20:09:18)
Saving to /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/01_assembly_reads.fastq:
  40 long reads

Finding overlaps with minimap... success
  120 overlaps

Assembling reads with miniasm... success
  7 segments, 6 links

    Unicycler removes any links from the string graph which create branches.
I.e. if any segment has two or more links connected to one end, those links are
removed. This will result in a graph with only simple linear paths that is
suitable for creating unambiguous bridges.

No links needed removal
Saving /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/11_branching_paths_removed.gfa
Merging segments into unitigs:

Linear unitig: 3708:125-4288- -> f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389-

  1 linear unitig
  total size = 5,836 bp
Saving /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/12_unitig_graph.gfa
Saving /corral4/main/jobs/045/766/45766274/working/002_unitig_graph.gfa


Polishing miniasm assembly with Racon (2022-09-15 20:09:18)
    Unicycler now uses Racon to polish the miniasm assembly. It does multiple
rounds of polishing to get the best consensus. Circular unitigs are rotated
between rounds such that all parts (including the ends) are polished well.

Saving to /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/racon_polish/polishing_reads.fastq:
  40 long reads

Polish       Assembly          Mapping
round            size          quality
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	210	4010	+	1	5836	1061	4603	1147	3800	255	cm:i:200
0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template	4286	129	722	+	1	5836	5221	5833	179	612	255	cm:i:27
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	934	4391	-	1	5836	2376	5833	3457	3457	255	cm:i:1153
054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template	4413	126	2525	-	1	5836	30	2314	787	2399	255	cm:i:144
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	280	4284	-	1	5836	4	3936	1481	4004	255	cm:i:246
3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template	4605	2719	4286	-	1	5836	4215	5833	546	1618	255	cm:i:88
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	170	4027	+	1	5836	1680	5833	1032	4153	255	cm:i:174
4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template	4127	2893	4082	+	1	5836	4	1602	220	1598	255	cm:i:30
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	1334	4566	-	1	5836	2699	5786	1281	3232	255	cm:i:243
598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template	4587	98	2778	-	1	5836	50	2663	772	2680	255	cm:i:129
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	1225	4611	-	1	5836	2657	5833	1469	3386	255	cm:i:268
771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template	4615	97	2786	-	1	5836	30	2636	905	2689	255	cm:i:157
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	143	4271	-	1	5836	338	4254	1834	4128	255	cm:i:470
9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template	4333	3092	4330	-	1	5836	4503	5798	430	1295	255	cm:i:77
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	544	4408	-	1	5836	69	3927	1208	3864	255	cm:i:237
9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template	4536	3008	4472	-	1	5836	4215	5748	351	1533	255	cm:i:53
a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template	433	106	396	+	1	5836	2909	3222	131	313	255	cm:i:22
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	335	4397	+	1	5836	1321	5257	1351	4062	255	cm:i:280
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	3437	4349	+	1	5836	23	961	238	938	255	cm:i:40
a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template	4456	86	537	+	1	5836	5334	5798	154	464	255	cm:i:26
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	111	4359	-	1	5836	1673	5798	2062	4248	255	cm:i:487
b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template	4435	109	1619	-	1	5836	30	1525	472	1510	255	cm:i:68
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	93	4048	+	1	5836	1733	5833	1303	4100	255	cm:i:230
bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template	4275	2532	4244	+	1	5836	4	1690	311	1712	255	cm:i:43
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	289	4205	+	1	5836	23	3939	1039	3916	255	cm:i:166
f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template	4509	296	1782	+	1	5836	4242	5798	367	1556	255	cm:i:63
begin           5,836             5.33

Best polish: /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/racon_polish/001_unpolished_unitigs.fasta
Saving /corral4/main/jobs/045/766/45766274/working/miniasm_assembly/13_racon_polished.gfa
Saving /corral4/main/jobs/045/766/45766274/working/003_racon_polished.gfa


Assembly complete (2022-09-15 20:09:30)
Saving /corral4/main/jobs/045/766/45766274/working/assembly.gfa


      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "false"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
4




Passed
0




Error
1




Failure
3




Skipped
0






Errored s




Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785982/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785982/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785982/command.sh: line 105: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/45785982/command.sh: line 105: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102810080, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102810084, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45786006/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45786006/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45786006/command.sh: line 105: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/45786006/command.sh: line 105: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102810080, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102810084, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785976/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785976/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45785976/command.sh: line 105: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/45785976/command.sh: line 105: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "false"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Sep 16, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
4




Passed
0




Error
1




Failure
3




Skipped
0






Errored s




Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790602/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790602/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790602/command.sh: line 105: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/45790602/command.sh: line 105: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102816295, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102816300, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Expecting value: line 1 column 1 (char 0)

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 102816295, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 102816300, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790592/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790592/command.sh: line 105: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/45790592/command.sh: line 105: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/45790592/command.sh: line 105: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "false"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Oct 4, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Oct 4, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
4




Passed
0




Error
0




Failure
4




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196467/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196467/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196467/command.sh: line 110: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46196467/command.sh: line 110: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 103516746, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 103516748, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196466/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196466/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196466/command.sh: line 110: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46196466/command.sh: line 110: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 103516746, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 103516748, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196472/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196472/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196472/command.sh: line 110: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46196472/command.sh: line 110: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 1, "fastq_input1": {"values": [{"id": 1727629, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "true"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "true"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196463/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196463/command.sh: line 110: pilon: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46196463/command.sh: line 110: pilon: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46196463/command.sh: line 110: pilon: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2", "no_correct": "false"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
pilon
{"min_polish_size": "1000", "no_pilon": "false"}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "scores": "3,-6,-5,-2"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Oct 6, 2022


      
  •

  

    
      

        
          edited
          
        
        
      

    
    
      
        
      Loading

      
    
  



    


  





      


        


  
    

      
          
Same error as a few reported bugs for this tool (this version).


A variation using toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0 produces an error like this:




stderr

/jetstream2/scratch/main/jobs/46230435/command.sh: line 110: unicycler: command not found




Tests for 0.4.8.0 passed on Oct4, tests for 0.5.0+galaxy0 started up

https://usegalaxy.org/u/jen/h/test-history-unicycler-train-data

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Oct 6, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Oct 6, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
7




Passed
0




Error
0




Failure
7




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236115/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236115/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236115/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/236/46236115/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 99574057, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 99574057, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236171/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236171/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236171/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/236/46236171/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 103594179, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 103594188, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236162/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236162/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236162/command.sh: line 110: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46236162/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 1, "fastq_input1": {"values": [{"id": 1730511, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236141/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236141/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/236/46236141/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/236/46236141/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236153/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236153/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236153/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46236153/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 103594179, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 103594188, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"1"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test trinotate 3.2.2+galaxy0 #6)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236151/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236151/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236151/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46236151/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46236151/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 103594179, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 103594188, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"2"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Problems:
    

      

    • 

      'command_line'

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Oct 20, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Oct 20, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
7




Passed
0




Error
0




Failure
7




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477133/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477133/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477133/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477133/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104175154, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104175161, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477135/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477135/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477135/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477135/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104175154, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104175161, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477138/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477138/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477138/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477138/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 1, "fastq_input1": {"values": [{"id": 1748973, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477129/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477129/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477129/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477129/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477132/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477132/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477132/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477132/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104175154, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104175161, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"1"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test trinotate 3.2.2+galaxy0 #6)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477134/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477134/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477134/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/046/477/46477134/tool_script.sh: line 10: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/046/477/46477134/tool_script.sh: line 10: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104175154, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104175161, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"2"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Problems:
    

      

    • 

      'command_line'

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Collaborator


      

  Author


  


  

    

      

      
            jennaj
  

      

      

      commented


        Oct 21, 2022


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Oct 21, 2022


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
7




Passed
0




Error
0




Failure
7




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test tool test #1)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490123/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490123/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490123/command.sh: line 110: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46490123/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104204129, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104204136, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test test against test.galaxyproject.org #2)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490117/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490117/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490117/command.sh: line 110: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46490117/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104204129, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104204136, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490118/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490118/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490118/command.sh: line 110: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46490118/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 1, "fastq_input1": {"values": [{"id": 1750125, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test roary 3.13.0+galaxy2 #4)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490120/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490120/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490120/command.sh: line 110: unicycler: command not found
.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46490120/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 3, "fastq_input_selector": "none"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
"10"

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"0"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Problems:
    

      

    • 

      Expecting value: line 1 column 1 (char 0)

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490119/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490119/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104204129, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104204136, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
long
None

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"1"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test trinotate 3.2.2+galaxy0 #6)
    

    Problems:
    

      

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490121/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490121/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490121/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/46490121/command.sh: line 110: unicycler: command not found
.

      

      • 

    • 

      Output collection 'spades_collection': expected to have 14 elements, but it had 0.

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /jetstream2/scratch/main/jobs/46490121/command.sh: line 110: unicycler: command not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
paired_unpaired
{"__current_case__": 0, "fastq_input1": {"values": [{"id": 104204129, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 104204136, "src": "hda"}]}, "fastq_input_selector": "paired"}

      

      
mode
"normal"

      

      
min_fasta_length
"100"

      

      
linear_seqs
"0"

      

      
min_anchor_seg_len
""

      

      
spades
{"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"}

      

      
rotation
{"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null}

      

      
graph_clean
{"min_component_size": "1000", "min_dead_end_size": "1000"}

      

      
lr_align
{"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"}

      

      
keep
"2"

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Problems:
    

      

    • 

      'command_line'

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Jan 17, 2023

    

  


    











  
  

    

      

  





  




  
  

              

  
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          @mvdbeek 
        
          @jennaj